IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell ...functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression and replication that depend on the structure and dynamics of its constituent proteins. Many protein structures ...have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate 0.1 seconds of the viral proteome. Our adaptive sampling simulations predict dramatic opening of the apo spike complex, far beyond that seen experimentally, explaining and predicting the existence of 'cryptic' epitopes. Different spike variants modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also discover dramatic conformational changes across the proteome, which reveal over 50 'cryptic' pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.
Social learning (learning through observation or interaction with other individuals) is widespread in nature and is central to the remarkable success of humanity, yet it remains unclear why copying ...is profitable and how to copy most effectively. To address these questions, we organized a computer tournament in which entrants submitted strategies specifying how to use social learning and its asocial alternative (for example, trial-and-error learning) to acquire adaptive behavior in a complex environment. Most current theory predicts the emergence of mixed strategies that rely on some combination of the two types of learning. In the tournament, however, strategies that relied heavily on social learning were found to be remarkably successful, even when asocial information was no more costly than social information. Social learning proved advantageous because individuals frequently demonstrated the highest-payoff behavior in their repertoire, inadvertently filtering information for copiers. The winning strategy (discountmachine) relied nearly exclusively on social learning and weighted information according to the time since acquisition.
The preferred timing of umbilical-cord clamping in preterm infants is unclear.
We randomly assigned fetuses from women who were expected to deliver before 30 weeks of gestation to either immediate ...clamping of the umbilical cord (≤10 seconds after delivery) or delayed clamping (≥60 seconds after delivery). The primary composite outcome was death or major morbidity (defined as severe brain injury on postnatal ultrasonography, severe retinopathy of prematurity, necrotizing enterocolitis, or late-onset sepsis) by 36 weeks of postmenstrual age. Analyses were performed on an intention-to-treat basis, accounting for multiple births.
Of 1634 fetuses that underwent randomization, 1566 were born alive before 30 weeks of gestation; of these, 782 were assigned to immediate cord clamping and 784 to delayed cord clamping. The median time between delivery and cord clamping was 5 seconds and 60 seconds in the respective groups. Complete data on the primary outcome were available for 1497 infants (95.6%). There was no significant difference in the incidence of the primary outcome between infants assigned to delayed clamping (37.0%) and those assigned to immediate clamping (37.2%) (relative risk, 1.00; 95% confidence interval, 0.88 to 1.13; P=0.96). The mortality was 6.4% in the delayed-clamping group and 9.0% in the immediate-clamping group (P=0.03 in unadjusted analyses; P=0.39 after post hoc adjustment for multiple secondary outcomes). There were no significant differences between the two groups in the incidences of chronic lung disease or other major morbidities.
Among preterm infants, delayed cord clamping did not result in a lower incidence of the combined outcome of death or major morbidity at 36 weeks of gestation than immediate cord clamping. (Funded by the Australian National Health and Medical Research Council NHMRC and the NHMRC Clinical Trials Centre; APTS Australian and New Zealand Clinical Trials Registry number, ACTRN12610000633088 .).
The National Compact Stellarator Experiment (NCSX) was designed to test a compact, quasi-axisymmetric stellarator configuration. Flexibility and accurate realization of its complex 3D geometry were ...key requirements affecting the design and construction. While the project was terminated before completing construction, there were significant engineering accomplishments in design, fabrication, and assembly. The design of the stellarator core device was completed. All of the modular coils, toroidal field coils, and vacuum vessel sectors were fabricated. Critical assembly steps were demonstrated. Engineering advances were made in the application of CAD modeling, structural analysis, and accurate fabrication of complex-shaped components and sub-assemblies. The engineering accomplishments of the project are summarized.
Beclin 1 is a haploinsufficient tumor suppressor that is decreased in many human tumors. The function of beclin 1 in cancer has been attributed primarily to its role in the degradative process of ...macroautophagy. However, beclin 1 is a core component of the vacuolar protein sorting 34 (Vps34)/class III phosphatidylinositoI-3 kinase (PI3KC3) and Vps15/p150 complex that regulates multiple membrane-trafficking events. In the current study, we describe an alternative mechanism of action for beclin 1 in breast cancer involving its control of growth factor receptor signaling. We identify a specific stage of early endosome maturation that is regulated by beclin 1, the transition of APPL1-containing phosphatidyIinositol 3-phosphate-negative (PI3P(-)) endosomes to PI3P(+) endosomes. Beclin 1 regulates PI3P production in response to growth factor stimulation to control the residency time of growth factor receptors in the PI3P(-)/APPL(+)-signaling-competent compartment. As a result, suppression of BECN1 sustains growth factor-stimulated AKT and ERK activation resulting in increased breast carcinoma cell invasion. In human breast tumors, beclin 1 expression is inversely correlated with AKT and ERK phosphorylation. Our data identify a novel role for beclin 1 in regulating growth factor signaling and reveal a mechanism by which loss of beclin 1 expression would enhance breast cancer progression.
Future searches for bio-markers on habitable exoplanets will rely on telescope instruments that achieve extremely high contrast at small planet-to-star angular separations. Coronagraphy is a ...promising starlight suppression technique, providing excellent contrast and throughput for off-axis sources on clear apertures. However, the complexity of space- and ground-based telescope apertures goes on increasing over time, owing to the combination of primary mirror segmentation, the secondary mirror, and its support structures. These discontinuities in the telescope aperture limit the coronagraph performance. In this paper, we present ACAD-OSM, a novel active method to correct for the diffractive effects of aperture discontinuities in the final image plane of a coronagraph. Active methods use one or several deformable mirrors that are controlled with an interaction matrix to correct for the aberrations in the pupil. However, they are often limited by the amount of aberrations introduced by aperture discontinuities. This algorithm relies on the recalibration of the interaction matrix during the correction process to overcome this limitation. We first describe the ACAD-OSM technique and compare it to the previous active methods for the correction of aperture discontinuities. We then show its performance in terms of contrast and off-axis throughput for static aperture discontinuities (segmentation, struts) and for some aberrations evolving over the life of the instrument (residual phase aberrations, artifacts in the aperture, misalignments in the coronagraph design). This technique can now obtain the Earth-like planet detection threshold of contrast on any given aperture over at least a 10% spectral bandwidth, with several coronagraph designs.
High-contrast imaging and spectroscopy provide unique constraints for exoplanet formation models as well as for planetary atmosphere models. Instrumentation techniques in this field have greatly ...improved over the last two decades, with the development of stellar coronagraphy, in parallel with specific methods of wavefront sensing and control. Next generation space- and ground-based telescopes will enable the characterization of cold solar-system-like planets for the first time and maybe even in situ detection of bio-markers. However, the growth of primary mirror diameters, necessary for these detections, comes with an increase of their complexity (segmentation, secondary mirror features). These discontinuities in the aperture can greatly limit the performance of coronagraphic instruments. In this context, we introduced a new technique, Active Correction of Aperture Discontinuities-Optimized Stroke Minimization (ACAD-OSM), to correct for the diffractive effects of aperture discontinuities in the final image plane of a coronagraph, using deformable mirrors. In this paper, we present several tools that can be used to optimize the performance of this technique for its application to future large missions. In particular, we analyzed the influence of the deformable setup (size and separating distance) and found that there is an optimal point for this setup, optimizing the performance of the instrument in contrast and throughput while minimizing the strokes applied to the deformable mirrors. These results will help us design future coronagraphic instruments to obtain the best performance.
Insulin secretion has a crucial role in glucose homeostasis, and failure to secrete sufficient insulin is a hallmark of type 2 diabetes. Genome-wide association studies (GWAS) have identified loci ...contributing to insulin processing and secretion; however, a substantial fraction of the genetic contribution remains undefined. To examine low-frequency (minor allele frequency (MAF) 0.5-5%) and rare (MAF < 0.5%) nonsynonymous variants, we analyzed exome array data in 8,229 nondiabetic Finnish males using the Illumina HumanExome Beadchip. We identified low-frequency coding variants associated with fasting proinsulin concentrations at the SGSM2 and MADD GWAS loci and three new genes with low-frequency variants associated with fasting proinsulin or insulinogenic index: TBC1D30, KANK1 and PAM. We also show that the interpretation of single-variant and gene-based tests needs to consider the effects of noncoding SNPs both nearby and megabases away. This study demonstrates that exome array genotyping is a valuable approach to identify low-frequency variants that contribute to complex traits.
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